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changeset 3:ab4c4e07eb3c

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Fix for using built-in reference data.
author Daniel Blankenberg <dan@bx.psu.edu>
date Fri, 17 Jan 2014 16:30:43 -0500
parents 05ca4081ca7e
children 8176b2575aa1
files sam_to_bam.py
diffstat 1 files changed, 0 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/sam_to_bam.py	Thu Jan 09 14:29:01 2014 -0500
+++ b/sam_to_bam.py	Fri Jan 17 16:30:43 2014 -0500
@@ -48,7 +48,6 @@
         # We're using locally cached reference sequences( e.g., /galaxy/data/equCab2/sam_index/equCab2.fa ).
         # The indexes for /galaxy/data/equCab2/sam_index/equCab2.fa will be contained in
         # a file named /galaxy/data/equCab2/sam_index/equCab2.fa.fai
-        fai_index_file_base = seq_path
         fai_index_file_path = '%s.fai' % options.index
         if not os.path.exists( fai_index_file_path ):
             #clean up temp files